&dhtitle;

&dhpackage;
&dhrelease;
&dhdate;
Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.

              chuongdo@cs.stanford.edu

&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.

              &dhemail;

This program and its manpage are in the public domain.

&dhucpackage; &dhsection;
&dhpackage; Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores.
`&dhpackage;` TEST_ALIGNMENT REFERENCE_ALIGNMENT BALIBASE_ANNOT_FILE `-col` `-core` `-caps` `-annot FILENAME`

## NOTE

&dhpackage; is named `compare` in the original sources, but has been remamed to avoid collision with other program names.

## SEE ALSO

pc-makegnufile 1 , pc-project 1 ,from the probcons-extra package, and probcons 1 and probcons-RNA 1 from the probcons package.

## REFERENCE

Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.